scholarly journals Theoretical and experimental study of interaction of macroheterocyclic compounds with ORF3a of SARS-CoV-2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Natalia Sh. Lebedeva ◽  
Yury A. Gubarev ◽  
Galina M. Mamardashvili ◽  
Svetlana V. Zaitceva ◽  
Sergey A. Zdanovich ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Viral Protein ◽  
Irreparable Harm ◽  
Exogenous Substance ◽  
Vis Spectroscopy ◽  
In Silico Modeling ◽  
The World ◽  
Macroheterocyclic Compounds ◽  
Virucidal Effect ◽  
Leading Compounds

AbstractThe pandemic infectious disease (Covid-19) caused by the coronavirus (SARS-CoV2) is spreading rapidly around the world. Covid-19 does an irreparable harm to the health and life of people. It also has a negative financial impact on the economies of most countries of the world. In this regard, the issue of creating drugs aimed at combating this disease is especially acute. In this work, molecular docking was used to study the docking of 23 compounds with QRF3a SARS-CoV2. The performed in silico modeling made it possible to identify leading compounds capable of exerting a potential inhibitory and virucidal effect. The leading compounds include chlorin (a drug used in PDT), iron(III)protoporphyrin (endogenous porphyrin), and tetraanthraquinone porphyrazine (an exogenous substance). Having taken into consideration the localization of ligands in the QRF3a SARS-CoV2, we have made an assumption about their influence on the pathogenesis of Covid-19. The interaction of chlorin, iron(III)protoporphyrin and protoporphyrin with the viral protein ORF3a were studied by fluorescence and UV–Vis spectroscopy. The obtained experimental results confirm the data of molecular docking. The results showed that a viral protein binds to endogenous porphyrins and chlorins, moreover, chlorin is a competitive ligand for endogenous porphyrins. Chlorin should be considered as a promising drug for repurposing.

scholarly journals Enzyme-Site Blocking Combined with Optimization of Molecular Docking for Efficient Discovery of Potential Tyrosinase Specific Inhibitors from Puerariae lobatae Radix

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2612 ◽  
Author(s):  
Haichun Liu ◽  
Yitian Zhu ◽  
Ting Wang ◽  
Jin Qi ◽  
Xuming Liu
Keyword(s):  
Molecular Docking ◽  
Structural Modification ◽  
Enzyme Inhibitors ◽  
Kojic Acid ◽  
Systematic Evaluation ◽  
Tyrosinase Inhibition ◽  
Computational Docking ◽  
Site Blocking ◽  
Leading Compounds ◽  
Positive Results

Enzyme inhibitors from natural products are becoming an attractive target for drug discovery and development; however, separating enzyme inhibitors from natural-product extracts is highly complex. In this study, we developed a strategy based on tyrosinase-site blocking ultrafiltration integrated with HPLC-QTOF-MS/MS and optimized molecular docking to screen tyrosinase inhibitors from Puerariae lobatae Radix extract. Under optimized ultrafiltration parameters, we previously used kojic acid, a known tyrosinase inhibitor, to block the tyrosinase active site in order to eliminate false-positive results. Using this strategy, puerarin, mirificin, daidzin and genistinc were successfully identified as potential ligands, and after systematic evaluation by several docking programs, the rank of the identified compounds predicted by computational docking was puerarin > mirificin > kojic acid > daidzin ≈ genistin, which agreed with the results of tyrosinase-inhibition assays. Structure-activity relationships indicated that C-glycosides showed better tyrosinase inhibition as compared with O-glycosides, with reduced inhibition achieved through the addition of glycosyl, which provides ideas about the screen of leading compounds and structural modification.

scholarly journals Molecular Docking Study of the Potential Relevance of the Natural Compounds Isoflavone and Myricetin to COVID-19

2021 ◽  
Vol 25 (3) ◽  
pp. 271-282
Author(s):  
Didik Priyandoko ◽  
◽  
Wahyu Widowati ◽  
Mawar Subangkit ◽  
Diana Jasaputra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
Active Sites ◽  
Docking Study ◽  
Binding Mode ◽  
Molecular Docking Study ◽  
Wuhan City ◽  
The World ◽  
Novel Coronavirus ◽  
Proteins Interactions

The 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly from its origin in Wuhan City, Hubei Province, China, to the rest of the world. The efficacy of herbal treatment in the control of contagious disease was demonstrated during the 2003 outbreak of severe acute respiratory syndrome (SARS). Natural compound used for this study were isoflavone and myricetin. Molecular docking was performed to analyze binding mode of the compounds towards 12 proteins related to COVID-19. The prediction shows that isoflavone and myricetin have moderate probability of antiviral activity. All of the docked compounds occupied the active sites of the proteins related to COVID-19. Based on QSAR and molecular docking, interactions were predicted with 10 out of 12 potential COVID-19 proteins for myricetin and with 9 out of 12 proteins interactions for isoflavone. A potential disease alleviating action is suggested for isoflavone and myricetin in the context of COVID-19 infection.

scholarly journals Molecular Docking Studies of Possible Treatment of Diabetes using Vasicine against Islet Amyloid Polypeptide

2021 ◽  
Vol 9 (VI) ◽  
pp. 4202-4209
Author(s):  
Tushar Kumar
Keyword(s):  
Type 2 Diabetes ◽  
Insulin Secretion ◽  
Molecular Docking ◽  
Islet Amyloid Polypeptide ◽  
Docking Studies ◽  
Islet Amyloid ◽  
Molecular Docking Studies ◽  
The World ◽  
Treatment Of Diabetes

Diabetes is the becoming one of the most common problem all over the world. About 1 in 10 persons are suffering from diabetes and most from type 2 diabetes. It occurs due to problem in pancreas which further results defect in the insulin secretion, as insulin maintains blood glucose level. The effect of Alpha-Amyrin Acetate, Myrcene and Vasicine compounds against Islet Amyloid polypeptide (IAPP) protein was seen through molecular docking studies. IAPP acts as complementary to insulin in regulating the sugar level for the treatment of diabetes disease by virtual screening. Different tools and software used in this research were Uniprot, Pubchem, Swiss ADMS, PyRx, Auto dock Vina/MGL tool and PyMOL.

scholarly journals Molecular docking analysis of netropsin and novobiocin with the viral protein targets HABD, MTD and RCD

2019 ◽  
Vol 15 (4) ◽  
pp. 233-239
Author(s):  
Afaf S. Alwabli ◽  
◽  
Sana G. Alattas ◽  
Alawiah M. Alhebshi ◽  
Nidal M. Zabermawi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Viral Protein ◽  
Protein Targets ◽  
Docking Analysis ◽  
Molecular Docking Analysis

Calix[4]pyrrole based Scrupulous probe for track on of tryptophan: Host-guest interaction, In silico modeling and molecular docking insights

2021 ◽  
pp. 111426
Author(s):  
Ajay L. Desai ◽  
Keyur D. Bhatt ◽  
Krunal M. Modi ◽  
Nihal P. Patel ◽  
Manthan Panchal ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
In Silico Modeling

In Silico Modeling of Spider Toxins: Bioinformatics, Molecular Docking, and Molecular Dynamics

Spider Venoms ◽  
2016 ◽  
pp. 205-221
Author(s):  
Moacyr Comar Jr ◽  
Vanildo Martins Lima Braga ◽  
Débora de Oliveira Lopes
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
In Silico ◽  
Spider Toxins ◽  
In Silico Modeling

scholarly journals Arsenate reductase from Thermus thermophilus conjugated to polyethylene glycol-stabilized gold nanospheres allow trace sensing and speciation of arsenic ions

2016 ◽  
Vol 13 (123) ◽  
pp. 20160629 ◽  
Author(s):  
Jane Politi ◽  
Jolanda Spadavecchia ◽  
Gabriella Fiorentino ◽  
Immacolata Antonucci ◽  
Luca De Stefano
Keyword(s):  
Gold Nanoparticles ◽  
Polyethylene Glycol ◽  
Environmental Problem ◽  
Thermus Thermophilus ◽  
Arsenate Reductase ◽  
Gold Nanospheres ◽  
Enzyme Adsorption ◽  
Ph Values ◽  
Vis Spectroscopy ◽  
The World

Water sources pollution by arsenic ions is a serious environmental problem all around the world. Arsenate reductase enzyme ( TtArsC ) from Thermus thermophilus extremophile bacterium, naturally binds arsenic ions, As(V) and As (III), in aqueous solutions. In this research, TtArsC enzyme adsorption onto hybrid polyethylene glycol-stabilized gold nanoparticles (AuNPs) was studied at different pH values as an innovative nanobiosystem for metal concentration monitoring. Characterizations were performed by UV/Vis and circular dichroism spectroscopies, TEM images and in terms of surface charge changes. The molecular interaction between arsenic ions and the TtArsC -AuNPs nanobiosystem was also monitored at all pH values considered by UV/Vis spectroscopy. Tests performed revealed high sensitivities and limits of detection equal to 10 ± 3 M −12 and 7.7 ± 0.3 M −12 for As(III) and As(V), respectively.

scholarly journals In-silico pharmacophore and Molecular Docking based drug discovery against Marburg Virus Viral Protein VP35; A potent of MAVD.

2021 ◽  
Author(s):  
Sameer Quazi ◽  
Shreelaxmi Gavas ◽  
Javed Ahmad Malik ◽  
Komal Singh Suman ◽  
Zeshan Haider
Keyword(s):  
Molecular Docking ◽  
Viral Protein ◽  
Virus Disease ◽  
Antiviral Drug ◽  
Computational Approach ◽  
Marburg Virus ◽  
Online Tool ◽  
Lipinski’S Rule ◽  
Zinc Database ◽  
Lipinski’S Rule Of Five

Marburg virus is a member of filoviridae and spreads severe Marburg hemorrhagic illness in humans and animals. Nowadays, there is no vaccine available that can completely stop the replication of Marburg replication. Therefore, this study is designed to repurpose the effective therapeutic antiviral drug by using a computational approach against exploring the mechanism of Marburg virus Viral protein 35. We have retrieved about 40570 drug-like small compounds from the ZINC database using the "ZINC Pharmer" online tool. Molecular docking of the ligands from the ready-to-dock database has been carried out using MOE. The five drugs have been identified to bind with VP35 possibly. A study was also performed to evaluate the drug-like characteristics of the substances for absorption, distribution, metabolism, and excretion (ADME). The findings clearly showed that ligands are interacting with the MARV VP35 protein. Interestingly, Lipinski's rule of five was observed by all ligands. These findings provide the foundation for reconstituting and utilizing molecules as a possible therapy for Marburg Virus Disease (MVD).

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating that they are potentials candidates for muti-target drugs for COVID-19.

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